A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the PavlidisLab/sc-annotation-pipeline analysis pipeline.
/space/grp/rschwartz/rschwartz/cell_annotation_cortex.nf/work/65/f35cff9b4c320a7934f63a75ea1735/GSE180670
Sample Outlier Composition (outliers)
Sample Outlier Composition (outliers) test.
Sample cell type composition
Sample cell type composition test.
Leiden Cluster Composition (outliers)
Leiden Cluster Composition (outliers) test.
Leiden cluster composition (cell types)
Leiden cluster composition (cell types) test.
Cell type markers
Cell type markers test.
Cell type markers table
Cell type markers table test.
| Sample Name | cell_type | class | family | markers |
|---|---|---|---|---|
| 0 | caudal ganglionic eminence derived GABAergic cortical interneuron | CGE | GABAergic | NR2F2 |
| 1 | lamp5 GABAergic cortical interneuron | CGE | GABAergic | LAMP5 |
| 2 | sncg GABAergic cortical interneuron | CGE | GABAergic | SNCG |
| 3 | vip GABAergic cortical interneuron | CGE | GABAergic | VIP |
| 4 | chandelier pvalb GABAergic cortical interneuron | MGE | GABAergic | COL25A1 |
| 5 | pvalb GABAergic cortical interneuron | MGE | GABAergic | PVALB |
| 6 | sst chodl GABAergic cortical interneuron | MGE | GABAergic | CHODL |
| 7 | sst GABAergic cortical interneuron | MGE | GABAergic | SST |
| 8 | Cajal-Retzius cell | Cajal-Retzius cell | Glutamatergic | RELN |
| 9 | corticothalamic-projecting glutamatergic cortical neuron | deep layer non-IT | Glutamatergic | FOXP2 |
| 10 | L5 ET neuron | deep layer non-IT | Glutamatergic | FEZF2 |
| 11 | near-projecting glutamatergic neuron | deep layer non-IT | Glutamatergic | TLE4 |
| 12 | L6 CT neuron | deep layer non-IT | Glutamatergic | NTSR1 |
| 13 | L6b neuron | deep layer non-IT | Glutamatergic | TOX2 |
| 14 | CA1-prosubiculum hippocampal neuron | Hippocampal | Glutamatergic | WFS1 |
| 15 | CA2-IG-FC hippocampal neuron | Hippocampal | Glutamatergic | RGS14 |
| 16 | CA3 hippocampal neuron | Hippocampal | Glutamatergic | GRIK4 |
| 17 | dentate gyrus hippocampal neuron | Hippocampal | Glutamatergic | CALB1 |
| 18 | subiculum hippocampal neuron | Hippocampal | Glutamatergic | GRM2 |
| 19 | L2/3 IT neuron | L2/3-6 IT | Glutamatergic | CUX1 |
| 20 | L4/5 IT neuron | L2/3-6 IT | Glutamatergic | RORB |
| 21 | L6 IT Car3 neuron | L2/3-6 IT | Glutamatergic | CAR3 |
| 22 | neural stem cell | Neuroglioblast | Neuroglioblast | SOX2 |
| 23 | neuroepithelial stem cell | Neuroglioblast | Neuroglioblast | PAX6 |
| 24 | CNS macrophage | CNS macrophage | Non-neuron | CD68 |
| 25 | microglial cell | CNS macrophage | Non-neuron | TMEM119 |
| 26 | astrocyte | Glia | Non-neuron | GFAP |
| 27 | ependymal cell | Glia | Non-neuron | FOXJ1 |
| 28 | oligodendrocyte | Glia | Non-neuron | MOG |
| 29 | OPC | Glia | Non-neuron | PDGFRA |
| 30 | CD8+ T cell | Immune | Non-neuron | CD8A |
| 31 | NK T cell | Immune | Non-neuron | NKG7 |
| 32 | T cell | Immune | Non-neuron | TRAC |
| 33 | pericyte | Mural | Non-neuron | RGS5 |
| 34 | smooth muscle cell | Mural | Non-neuron | MYH11 |
| 35 | leptomeningeal cell | Stromal | Non-neuron | LUM |
| 36 | endothelial cell | Vascular | Non-neuron | VWF |